VACCINE DEVELOPMENT - Enhancing Pandemic Preparedness With Mosaic-8b Nanoparticles

INTRODUCTION

Vaccines have long been pivotal tools in controlling infectious diseases, significantly decreasing the global disease burden by helping to prevent illness, reduce transmission, and protect vul­nerable populations. Most importantly, immunization has saved countless lives over the years by preventing severe outcomes, par­ticularly in diseases with high mortality rates, such as smallpox, measles, and tuberculosis. These benefits were brought sharply into focus during the recent COVID-19 pandemic, when the rapid development and distribution of vaccines played a significant role in mitigating the spread of the virus. Today, vaccine research is advancing further with the development of a broad-spectrum vac­cine providing cross-reactive immunity against both current and future strains of sarbecoviruses. This innovative preventive treat­ment strategy has the potential to boost global resilience against future outbreaks.

ADDRESSING GAPS IN THE CURRENT VACCINE LANDSCAPE

The COVID-19 pandemic demonstrated the transformative power of vaccines in safeguarding global health. Despite over 7 million reported COVID-related deaths since January 2020 – a number that continues to increase daily – the rapid development and rollout of vaccines has saved countless lives.¹ Estimates sug­gest that COVID-19 vaccines prevented approximately 20 million deaths worldwide in their first year of availability alone.² Since then, they have helped to reduce the overall risk of death by as much as 57%, providing a critical line of defense against the virus’s spread.³ However, the natural tendency for viruses to mu­tate poses ongoing challenges, making it difficult for immunolo­gists to keep pace.

An Evolving Challenge
Most current COVID-19 vaccines work by presenting frag­ments of the SARS-CoV-2 spike protein to the body, allowing the immune system to recognize and fight off the virus. This mode of action proved highly effective during the initial vaccine rollout, leading to widespread immunity. However, RNA viruses like SARS-CoV-2 have a highly error-prone replication process and are therefore likely to have high mutation rates.⁴ This results in the production of new viral strains with altered antigenic epitopes – regions on the surface of the virus that the immune system rec­ognizes and targets. When these epitopes change, existing anti­bodies may not recognize or bind to the virus with the same affinity, reducing the immune system’s ability to neutralize the virus and allowing it to evade a previously effective immune re­sponse. For instance, substitutions in the SARS-2 spike protein re­ceptor-binding domains (RBDs) of the Omicron variant have reduced the efficacies of both vaccines and therapeutic mono­clonal antibodies, leading to breakthrough infections in individ­uals previously immune to the original strain.^5,6  Continuing viral evolution may therefore mean that current vaccines struggle to provide sustained protection, as they were designed to target ear­lier versions of the virus.⁷ This emphasizes the need for updated or alternative vaccine strategies that can generate neutralizing antibodies capable of effectively targeting emerging variants.

A Temporary Fix
At the peak of the COVID-19 pan­demic, developing variant-specific boost­ers was a necessary approach to help extend protection against evolving viral strains. The severity of the pandemic prompted swift action, with the US govern­ment alone investing at least $31.9 billion to accelerate the development, production, and purchase of mRNA vaccines against SARS-CoV-2.⁸ This substantial investment allowed researchers to formulate, test, and distribute the first doses of both the initial and booster vaccines in record time. How­ever, constantly updating vaccine formula­tions to combat emerging viral variants is not a sustainable long-term solution. De­veloping and refining vaccine candidates is a time-consuming and resource-inten­sive process that can take months or longer, so constantly creating new boosters for each variant would be costly and logis­tically challenging. Additionally, the rapid pace of viral mutations may outstrip the ability of manufacturers to produce up­dated vaccines in time, making it difficult to keep up with the evolving virus.

The Ongoing Need for a Broader Solution
A more viable long-term approach would be a universal vaccine capable of offering broad protection against both cur­rent SARS-CoV-2 variants and emerging sarbecoviruses, eliminating the need for constant reformulation. This solution ad­dresses the limitations of traditional vac­cines by targeting more stable, conserved regions of the RBDs less prone to muta­tion, which are shared by all existing viruses in the SARS-like betacoronavirus family. The benefits of a universal vaccine are clear: not only would it reduce the fre­quency of necessary updates, but it would also ensure more consistent protection, better equipping public health systems to manage rapidly evolving viral threats.

CLOSING THE IMMUNITY GAP

The need to develop a broad-spec­trum vaccine has sparked an international consortium – including the California In­stitute of Technology (Caltech), the Univer­sity of Oxford, engineering biology CRDMO Ingenza, and the UK-based Cen­tre for Process Innovation (CPI) – to initiate development of a novel next generation vaccine against known and future SARS-CoV-2 strains. The principle behind this in­novative vaccine project – led by Professor Pamela J. Bjorkman and her team at Cal­tech, and funded by The Coalition for Epi­demic Preparedness Innovations (CEPI) – focuses on directing the immune response toward conserved regions of the RBD shared by viruses in the SARS-like beta­coronavirus genus, particularly all sarbe­coviruses. This strategy aims to provide broad-spectrum immunity against multiple coronavirus strains, including emerging SARS-CoV-2 variants.

A BIOMANUFACTURING BREAKTHROUGH

The aim of this project is to advance Caltech’s ‘mosaic-8b’ nanoparti­cle vaccine candidate, which consists of protein-based, self-assembling 60-mer nanoparticles with RBDs from SARS-CoV-2 and seven other coronaviruses arranged randomly on their surface. The key advan­tage of this design is that it reduces the probability of two adjacent RBDs on the nanoparticle being identical, therefore fa­voring interactions with B cells with recep­tors that can preferentially recognize RBD regions conserved across a broad range of coronaviruses. Because these regions should be present and unchanged in all SARS-CoV-2 variants currently in circula­tion and novel variants that may emerge in the future, as well as other undiscovered sarbecoviruses, mosaic-8 RBD-nanoparti­cles show promise as a broad-spectrum vaccine candidate.

Initial research published by Caltech and Oxford in 2022 confirmed that these nanostructures effectively elicit protective immune responses against the SARS-like betacoronaviruses that correspond to the components displayed on the nanoparti­cles, as well as against other related viruses not represented in the mosaic-8b design.⁹ This includes coronaviruses found in animals that could pose a risk of zoonotic transfer in the future. Given that the spillover of animal sarbecoviruses has led to two major outbreaks over the past 20 years – the SARS-1 pandemic in the early 2000s, followed by the COVID-19 pandemic – preventing cross-species transmission is critical for strengthening global pandemic preparedness.

MOVING AWAY FROM CONVENTIONAL HOST PLATFORMS

Ingenza’s role in the project was to develop and optimize production of the vaccine components. The biopharmaceu­tical candidate was initially produced using two common biomanufacturing platforms: mammalian cells for the RBD components and Escherichia coli for the nanoparticle scaffold. Mammalian cells are highly ef­fective for producing complex proteins and replicating human biological processes, making them ideal for generating biolog­ically active compounds. However, they also require expensive media – hindering large-scale production of the eight antigen components required for this vaccine can­didate – and have a slow turnaround time, which poses a challenge in responding to fast-mutating viruses like SARS-CoV-2. E. coli offers faster cell growth and simpler processes, but requires cell lysis and exten­sive downstream processing to purify the nanoparticle from the host cell proteins and contaminating endotoxins.

To address these limitations, Ingenza transitioned production of the mosaic-8b candidate to the yeast Pichia pastoris and the Gram-positive bacteria Bacillus subtilis. These microbial platforms offer quicker production cycles, simpler culturing condi­tions, and the ability to secrete correctly folded recombinant proteins. This makes the production process more efficient and cost effective, leading to a more afford­able and accessible vaccine without com­promising on quality.

ENHANCING BIOPROCESS DEVELOPMENT

Ingenza harnessed its proprietary in­Genius™ platform to streamline the vac­cine production process, efficiently guiding each step from the creation of custom mi­crobial strains to the development of scal­able bioprocesses and generation of material required for preclinical Good Laboratory Practice (GLP) toxicology stud­ies. The platform integrates several mod­ules designed to optimize bioprocess development by selecting the best DNA design and production hosts. Additionally, the inGenius platform incorporates essen­tial analytical methods for in-process con­trols, release assays and drug substance characterization. Centralizing vaccine de­velopment within an integrated platform offers a more efficient, predictable, and scalable bioprocess, and decreases the risks typically associated with biopharma­ceutical production. It therefore provides a fast, reliable, and cost-effective pathway to market, reducing the costs associated with traditional biomanufacturing processes.

BUILDING ON EXISTING VACCINE IMMUNITY

The widespread transmission of SARS-CoV-2 following the most recent pandemic means that a significant portion of the population has likely encountered the virus by now.9 This makes it especially important for new vaccines to induce ef­fective immune responses in individuals with previous exposure to the disease or following prior vaccination.

Targeting Various Viral Strains
In the summer of 2022, the mosaic-8b vaccine project secured additional funding and entered extensive preclinical trials to test its ability to generate an im­mune response in individuals who are not immunologically naïve. The trials demon­strated that mosaic-8b nanoparticles effec­tively induce production of two types of antibodies: recall antibodies, which boost the immune system’s existing defenses, and cross-reactive de novo antibodies ca­pable of targeting a broad range of sar­becoviruses, including those more distantly related to SARS-CoV-2. These antibodies were more effective at recognizing differ­ent viral strains compared to those trig­gered by eight homotypic nanoparticles in the admixture. Additionally, they showed stronger binding and neutralizing abilities than antibodies generated following vac­cination with conventional SARS-CoV-2 vaccines, indicating that the mosaic-8b candidate is more versatile in fighting a wider range of viruses.

Overcoming Original Antigenic Sin
The preclinical trials also offered valu­able insights into the phenomenon of orig­inal antigenic sin (OAS), where the immune system tends to rely on memory cells formed during an initial exposure to the virus when encountering related anti­gens.¹⁰  This can limit the immune system’s ability to respond effectively to new vari­ants. The mosaic-8b vaccine showed promise in overcoming this issue, by gen­erating new antibodies that target a range of sarbecovirus RBDs, rather than merely enhancing the production of existing anti­bodies specific to certain SARS-CoV-2 strains. These findings suggest that a sin­gle dose of this vaccine could stimulate a stronger and broader immune response in individuals who are not immunologically naïve compared to a single dose of a stan­dard SARS-CoV-2 homotypic vaccine. This would mean longer-lasting protection against a wider range of SARS-CoV-2 strains and other sarbecoviruses.

SUMMARY

Although the mosaic-8b vaccine is still in early development, it has the potential to enable a broad and cross-reactive im­munization strategy that could provide comprehensive protection against known and unknown sarbecoviruses. The mosaic-8b nanostructure could also serve as a template for developing next generation vaccines that do not need frequent up­dates or iterations, unlike monovalent or bivalent vaccines targeting specific vari­ants. The next phase of this groundbreak­ing project is to advance the mosaic-8b vaccine candidate into the final round of preclinical trials, with the goal of entering human clinical trials in the near future, moving closer to a market-ready vaccine. With a multi-pronged defense system that is resilient to viral escape, this next gener­ation vaccination strategy can enhance our protection against various viral strains, both now and in the future.

REFERENCES

1. World Health Organization. (2024). WHO covid dashboard. https://data.who.int/dashboards/covid19/deaths.
2. Watson, O.J. et al. (2022). Global impact of the first year of COVID-19 vaccination: A mathematical modelling study. The Lancet Infectious Diseases, 22(9), 1293-1302. doi: 10.1016/s1473-3099(22)00320-6.
3. World Health Organization. (2024). COVID-19 vaccinations have saved more than 1.4 million lives in the WHO European Region, a new study finds. https://www.who.int/europe/news/item/16-01-2024-covid-19-vaccinations-have-saved-more-than-1.4-million-lives-in-the-who-european-region-a-new-study-finds.
4. Sanjuán, R., & Domingo-Calap, P. (2016). Mechanisms of viral muta­tion. Cellular and molecular life sciences: CMLS, 73(23), 4433-4448. doi: 10.1007/s00018-016-2299-6.
5. Willett, B.J., Grove, J., MacLean, O.A. et al. (2022). SARS-CoV-2 Omi­cron is an immune escape variant with an altered cell entry pathway. Nature Microbiology, 7, 1161-1179. doi: 10.1038/s41564-022-01143-7.
6. Bergwerk, M., Gonen, T., Lustig, Y., et al. (2021). COVID-19 Break­through Infections in Vaccinated Health Care Workers. The New Eng­land journal of medicine, 385(16), 1474-1484. doi: 10.1056/NEJMoa2109072.
7. Beukenhorst, A. L., Koch, C. M., Hadjichrysanthou, C., et al. (2023). SARS-CoV-2 elicits non-sterilizing immunity and evades vaccine-in­duced immunity: implications for future vaccination strategies. Euro­pean journal of epidemiology, 38(3), 237-242. doi: 10.1007/s10654-023-00965-x.
8. Lalani, H.S., Nagar, S., Sarpatwari, A., et al. (2023). US public invest­ment in development of mRNA COVID-19 vaccines: retrospective co­hort study. BMJ (preprint). doi: 10.1136/bmj-2022-073747.
9. Cohen, A. A., van Doremalen, N., Greaney, A. J., et al. (2022). Mosaic RBD nanoparticles protect against challenge by diverse sarbecoviruses in animal models. Science, 377(6606), eabq0839.
10. Cohen, A. A., Keeffe, J. R., Schiepers, A., et al. (2024). Mosaic sarbe­covirus nanoparticles elicit cross-reactive responses in pre-vaccinated animals. Cell (published online ahead of print), 187, 1-18. doi: 10.1016/j.cell.2024.07.052.

Dr. Leonardo Magneschi is Vice President of Research and Technology Development at Ingenza. He has more than 15 years of experience in microbiology and genetic engineering, with a PhD in Plant and Microbial Biotechnology, 17 published papers in peer-reviewed scientific journals, and inventorship on several international patents. He joined Ingenza in 2016 and has since been directly involved in a multitude of customer projects, with applications ranging from pharma and biofuels to renewable materials. He can be reached at Leonardo.magneschi@ingenza.com.